Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	850,389	T→C	intergenic (‑292/‑61)	rhtA ← / → ompX	threonine and homoserine efflux system/outer membrane protein X

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	850,389	0	T	C	100.0%	154.8 / NA	46	intergenic (‑292/‑61)	rhtA/ompX	threonine and homoserine efflux system/outer membrane protein X
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (24/22);  total (24/22)

GATGAATGACAGGGAAAACATGCGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTTCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAGGTACTTCCGTAGCTGCGAC  >  NC_000913/850253‑850523                                                                                                                                         |                                                                                                                                       gATGAATGACAGGGAAAACATGCGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTccc                                                                                                                                      >  2:82203/1‑139 (MQ=255)            gggAAAACATGCG‑‑‑TACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGat                                                                                                                        <  2:154963/139‑1 (MQ=255)             ggAAAACATGCGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTg                                                                                                                          <  2:206340/139‑1 (MQ=255)              gAAAACATGCGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGa                                                                                                                         <  1:82203/139‑1 (MQ=255)                                 aCGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGAc                                                                                                      >  1:171152/1‑139 (MQ=255)                                       ttCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTa                                                                                                                 >  1:1397659/1‑122 (MQ=255)                                       ttCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTa                                                                                                                 <  2:1397659/122‑1 (MQ=255)                                                 aaGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACAtt                                                                                      >  2:292782/1‑139 (MQ=255)                                                                          cGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCa                                                             >  1:922680/1‑139 (MQ=255)                                                                            ttgtATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATg                                                           <  2:922680/138‑1 (MQ=255)                                                                               tATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACtt                                                                                                           >  1:1061198/1‑88 (MQ=255)                                                                               tATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACtt                                                                                                           <  2:1061198/88‑1 (MQ=255)                                                                               tATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCt                                                        >  1:465095/1‑139 (MQ=255)                                                                               tATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCt                                                        >  1:973073/1‑139 (MQ=255)                                                                                    aaaCGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAg                                                   >  2:1363801/1‑139 (MQ=255)                                                                                       cGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGat                                                                                                                        <  1:847876/67‑1 (MQ=255)                                                                                       cGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGat                                                                                                                        >  2:847876/1‑67 (MQ=255)                                                                                       cGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACt                                                                                                            <  1:743902/79‑1 (MQ=255)                                                                                       cGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACt                                                                                                            >  2:743902/1‑79 (MQ=255)                                                                                       cGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATg                                                           >  1:676072/1‑128 (MQ=255)                                                                                       cGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATg                                                           <  2:676072/128‑1 (MQ=255)                                                                                       cGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCAc                                                >  2:765903/1‑139 (MQ=255)                                                                                         ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTaa                                                                                                                                >  2:1403601/1‑57 (MQ=255)                                                                                         ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTaa                                                                                                                                <  1:1403601/57‑1 (MQ=255)                                                                                         ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTTATATATTTAAAACTTAGGACTTATTTGAATCAGATTTGAGGTGGTTATGAAAAAAAATGCATGTCTTTGAGCACTg                                              >  2:996069/1‑139 (MQ=255)                                                                                         ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGTTGTTTATGAAAAAAATTGCATGTCTTTCAGCACTg                                              >  2:621696/1‑139 (MQ=255)                                                                                         ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTg                                              >  1:928440/1‑139 (MQ=255)                                                                                         ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTg                                              >  1:226170/1‑139 (MQ=255)                                                                                           cTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCa                                                             >  1:909916/1‑122 (MQ=255)                                                                                           cTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCa                                                             <  2:909916/122‑1 (MQ=255)                                                                                                   tGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTc                                    <  2:973073/139‑1 (MQ=255)                                                                                                           cccGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTa                                                                                                                 <  2:937270/54‑1 (MQ=255)                                                                                                           cccGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGa                                                                                                       <  1:354712/64‑1 (MQ=255)                                                                                                           cccGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGa                                                                                                       >  2:354712/1‑64 (MQ=255)                                                                                                           cccGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt                                                                                            <  2:217934/75‑1 (MQ=255)                                                                                                           cccGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt                                                                                            >  1:217934/1‑75 (MQ=255)                                                                                                           cccGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTc                            >  1:1014240/1‑139 (MQ=255)                                                                                                           cccGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATGTTTGATATATTTa                                                                                                                 >  1:937270/1‑54 (MQ=255)                                                                                                              gTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCAcc                         <  1:1363801/139‑1 (MQ=255)                                                                                                               ttAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGtt                                                                            >  2:33270/1‑87 (MQ=255)                                                                                                               ttAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGtt                                                                            <  1:33270/87‑1 (MQ=255)                                                                                                                 aGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTCTCACCGCa                      <  1:996069/139‑1 (MQ=255)                                                                                                                 aGACATCACAAATCGCGAAGACTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCa                      <  1:837598/139‑1 (MQ=255)                                                                                                                               gcgAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAGGTACTTCCGTAGc        >  1:357847/1‑139 (MQ=255)                                                                                                                                  aaGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAGGTACTTCCGTAGCTGc     <  2:357847/139‑1 (MQ=255)                                                                                                                                  aaGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAGGTACTTCCGTAGCTGc     <  2:1014240/139‑1 (MQ=255)                                                                                                                                     agTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAGGTACTTCCGTAGCTGCGAc  <  1:105518/139‑1 (MQ=255)                                                                                                                                         |                                                                                                                                       GATGAATGACAGGGAAAACATGCGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTTCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAGGTACTTCCGTAGCTGCGAC  >  NC_000913/850253‑850523

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑